Searching for common sequence patterns among distantly related proteins
نویسندگان
چکیده
منابع مشابه
NdPASA: a pairwise sequence alignment server for distantly related proteins
SUMMARY NdPASA is a web server specifically designed to optimize sequence alignment between distantly related proteins. The program integrates structure information of the template sequence into a global alignment algorithm by employing neighbor-dependent propensities of amino acids as a unique parameter for alignment. NdPASA optimizes alignment by evaluating the likelihood of a residue pair in...
متن کاملPROMALS: towards accurate multiple sequence alignments of distantly related proteins
MOTIVATION Accurate multiple sequence alignments are essential in protein structure modeling, functional prediction and efficient planning of experiments. Although the alignment problem has attracted considerable attention, preparation of high-quality alignments for distantly related sequences remains a difficult task. RESULTS We developed PROMALS, a multiple alignment method that shows promi...
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Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), whi...
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MOTIVATION Although many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever. RESULTS Using principal component analysis wi...
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Photosynthesis was established on Earth more than 3 billion years ago. All available evidences suggest that the earliest photosynthetic organisms were anoxygenic and that oxygen-evolving photosynthesis is a more recent development. The reaction center complexes that form the heart of the energy storage process are integral membrane pigment proteins that span the membrane in vectorial fashion to...
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ژورنال
عنوان ژورنال: "Protein Engineering, Design and Selection"
سال: 1995
ISSN: 1741-0126,1741-0134
DOI: 10.1093/protein/8.11.1075